Cal Poly students and faculty are working together to build a library of DNA fingerprints to identify the culprit when people get sick fromĀ E. coli. In 2007, health officials posted notices in Pismo Beach because of a high increase inĀ E. coliĀ levels, biological sciences chair Christopher KittsĀ said.
E. coliĀ is a bacterium that comes from a variety of sources, but itās found in the same place. The bacterium is present in the guts of humans and animals, said Anya Goodman, chemistry and biochemistry professor.
āE. coliĀ is just kind of used an indicator of fecal contamination, because normally people donāt just expect it to be found in the environment as a free living thing,ā Goodman said. āItās bacteria that lives in the gut.ā
Identifying the source ofĀ E. coliĀ can get complicated. Kitts, faculty and students are researching how to better identify the source ofĀ E. coliĀ to reduce its presence in local waters.
Sometimes the bacteria pass from one animal to another and then into the water, Goodman said.
āPart of the problem is they can be interchangeable,” Goodman said. “So Iāve heard stories that thereās exchange ofĀ E. coliĀ between seagulls feeding on trashed, poopy diapers. So part of what weāre trying to figure out is what are some of the host specificĀ E. coliĀ and can we use them to track the sources of contamination.ā
Just as each person has a different fingerprint, eachĀ E. coliĀ is a little different from species to species, Goodman said.
āItās really easy to say āthis isĀ E. coliāĀ or ānotĀ E. coli,’ but itās really hard to distinguish differentĀ E. coliās from each other,ā Goodman said.
The team is researching to find a simpler, yet accurate method of testing and identifyingĀ E. coliĀ sources, Kitts said. E. coliĀ isĀ E. coli, but birdĀ E. coliĀ will have a different molecular fingerprint than dogĀ E. coli.
Students in biology professor Michael Blacksā BIO 161, Introduction to Cell and Molecular Biology, class are analyzing samples ofĀ E. coliĀ to add fingerprints to the library. Without the initial sample, the library wouldnāt have data to compare E. coliĀ to.
āThe fingerprinting method that we have developed here is novel,ā Black said.
The method was developed by a team of faculty members at Cal Poly and is being practiced by students in freshmen and sophomore biology classes.
āPyroprinting is a method that allows us to determine the sequence of a DNA strand,” Black said. “DNA is based on four different letters which represent nucleotides that make up the strand. As enzymes incorporate a letter, a pyrophosphate is released as a byproduct of the reaction. Other enzymes in the mix use this pyrophosphate to convert chemical energy into light energy ā the same enzymes that make fireflies glow. This means that each times a letter is added, light is given off and can be detected by the machine.ā
The National Science Foundation initially turned Cal Poly down for a grant because there was a lot of mistrust in the accuracy of the students’ work. Cal Poly demonstrated that not only can undergraduate students collect, properly isolate and test a sample forĀ E. coli, but that they can perform the same tests and produce the same results with very little variation, Goodman said.
āWe designed a study where there are triplicate repeats, so three students do the same thing and we can show āYeah, they can do real science. They can do it.ā Thatās partly why we ended up getting this grant,ā Goodman said. āThe first time there was a lot of mistrust and we said, āLook, weāre doing it. Our students are that good, they can handle this.āā
With the new method for analyzing DNA, itās possible for even freshman-level undergraduate students to perform the same type of tests that are conducted in large testing laboratories.
āWe can distinguish between very closely related bacteria,ā Black said.
While the fingerprint library is still a work in progress, it gives students an opportunity to practice real world techniques and be a part of a newly evolving method for identifying and sequencing bacteria DNA, Goodman said.
āThe tools theyāre using and the statistical analysis that theyāre using and the exposure to database type research is all very valuable and applicable to a variety of different things,ā Black said.
Professor Janelle Barbierās students in General Microbiology I (MCRO 224) are testing samples collected by other biology classes and isolatingĀ E. coliĀ to be analyzed and added to the library.
“Learning microbiology techniques not only helps build the library, but these are all standard tests and are used in a variety of disciplines” Barbier said.
Doing real world work gives Cal Poly students an advantage, Black said. Putting the research into the fingerprint library will help scientists pinpoint the source of contamination.
āIf we can figure out the source of theĀ E. coli, we can halt that transmission, if possible,ā Black said.
Megan Stone contributed to this article.